Dear Shankar,
Normally users develop scripts to run multiple FAST simulations e.g. to simulate multiple wind conditions for the same wind turbine. This has been discussed several times on this forum e.g. NWTC Design Codes - General Questions.
By a *.wnd file, presumably you mean the turbulent wind data file in binary format. (The turbulent wind binary file in Bladed format typically has the *.wnd extension.) However, unless you plan to use Bladed, I would recommend using the TurbSim binary format *.bts. Regardless, both types of turbulent wind data files can be generated using TurbSim: nwtc.nrel.gov/turbsim.
Best regards,